2VQ4 | pdb_00002vq4

Carbohydrate-binding of the starch binding domain of Rhizopus oryzae glucoamylase in complex with beta-cyclodextrin and maltoheptaose

• PDB DOI: https://doi.org/10.2210/pdb2VQ4/pdb

• Classification: HYDROLASE
• Organism(s): Rhizopus arrhizus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-03-11 Released: 2009-07-07 
• Deposition Author(s): Tung, J.-Y., Liu, Y.-Y., Sun, Y.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of the Starch-Binding Domain from Rhizopus Oryzae Glucoamylase Reveal a Polysaccharide-Binding Path.

Tung, J.-Y., Chang, M.D., Chou, W., Liu, Y.-Y., Yeh, Y., Chang, F., Lin, S., Qiu, Z., Sun, Y.-J.

(2008) Biochem J 416: 27

• PubMed: 18588504 
• DOI: https://doi.org/10.1042/BJ20080580
• Primary Citation Related Structures: 
  2V8L, 2V8M, 2VQ4


• PubMed Abstract: 
  

  GA (glucoamylase) hydrolyses starch and polysaccharides to beta-D-glucose. RoGA (Rhizopus oryzae GA) consists of two functional domains, an N-terminal SBD (starch-binding domain) and a C-terminal catalytic domain, which are connected by an O-glycosylated linker. In the present study, the crystal structures of the SBD from RoGA (RoGACBM21) and the complexes with beta-cyclodextrin (SBD-betaCD) and maltoheptaose (SBD-G7) were determined. Two carbohydrate binding sites, I (Trp(47)) and II (Tyr(32)), were resolved and their binding was co-operative. Besides the hydrophobic interaction, two unique polyN loops comprising consecutive asparagine residues also participate in the sugar binding. A conformational change in Tyr(32) was observed between unliganded and liganded SBDs. To elucidate the mechanism of polysaccharide binding, a number of mutants were constructed and characterized by a quantitative binding isotherm and Scatchard analysis. A possible binding path for long-chain polysaccharides in RoGACBM21 was proposed.

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Organizational Affiliation: 
• Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 11.66 kDa 
• Atom Count: 1,046 
• Modeled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOAMYLASE A	A	106	Rhizopus arrhizus	Mutation(s): 1  EC: 3.2.1.3
UniProt
Find proteins for Q2VC81 (Rhizopus oryzae) Explore Q2VC81  Go to UniProtKB:  Q2VC81

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.635	α = 90
b = 33.894	β = 90
c = 93.389	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Tung, J.-Y., Liu, Y.-Y., Sun, Y.-J.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description